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A Y-STR is a
short tandem repeat A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organism's genome ...
(STR) on the
Y-chromosome The Y chromosome is one of two sex chromosomes (allosomes) in therian mammals, including humans, and many other animals. The other is the X chromosome. Y is normally the sex-determining chromosome in many species, since it is the presence or abse ...
. Y-STRs are often used in
forensic Forensic science, also known as criminalistics, is the application of science to Criminal law, criminal and Civil law (legal system), civil laws, mainly—on the criminal side—during criminal investigation, as governed by the legal standard ...
s, paternity, and
genealogical DNA test A genealogical DNA test is a DNA-based test used in genetic genealogy that looks at specific locations of a person's genome in order to find or verify ancestral genealogical relationships, or (with lower reliability) to estimate the ethnic mixt ...
ing. Y-STRs are taken specifically from the male Y chromosome. These Y-STRs provide a weaker analysis than autosomal STRs because the Y chromosome is only found in males, which are only passed down by the father, making the Y chromosome in any paternal line practically identical. This causes a significantly smaller amount of distinction between Y-STR samples. Autosomal STRs provide a much stronger analytical power because of the random matching that occurs between pairs of chromosomes during the zygote making process.


Nomenclature

Y-STRs are assigned names by the
HUGO gene nomenclature committee The HUGO Gene Nomenclature Committee (HGNC) is a committee of the Human Genome Organisation (HUGO) that sets the standards for human gene nomenclature. The HGNC approves a ''unique'' and ''meaningful'' name for every known human gene, based on a ...
(HGNC). Some testing companies have different formats for the way STR markers are written. For example, the marker DYS455 may be written as DYS455, DYS 455, DYS#455, or DYS# 455. The scientific standard accepted by HUGO and
NIST The National Institute of Standards and Technology (NIST) is an agency of the United States Department of Commerce whose mission is to promote American innovation and industrial competitiveness. NIST's activities are organized into physical sci ...
is DYS455.


DYS

DYS is a variation on the jargon used in human autosomal STR testing where the second character is typically reserved for the chromosome number (e.g. D8S1179). D = DNA
Y = Y-chromosome
S = (unique) segment


Y-STR analysis

There are regions on DNA that are made up of multiple copies of short repeating sequences of bases (for example TATT) which repeat a variable number of times depending on the individual. These regions, called “variable number short tandem repeats” are what is looked at when performing STR analysis. The likelihood of two people having the same number of repeated sequences is extremely small, and becomes even smaller the more regions that are analyzed. This makes up the basis of short tandem repeat analysis. The cornerstone for this process, however, is polymerase chain reaction (PCR). This allows forensic scientists to make millions of copies of the STR regions. Gel electrophoresis then “yields the number of times each repeat unit appears in the fragment.” This allows for easy comparison of DNA.


STRs and forensics

In the United States, 13 different autosomal STR loci are used as a basis of analysis for forensic purposes. If crime scene DNA is ample and all 13 autosomal loci accessible, the likelihood of two unrelated people matching the same sample is around one in one billion. The basis for the profile probability estimation for Y-STR analysis is the counting method. The application of a confidence interval accounts for database size and sampling variation. The Y haplotype frequency (p) is calculated using the p = x/N formula, where x is equal to the number of times the haplotype is observed in a database containing N number of haplotypes. For example, if a haplotype has been observed twice in a database of N = 2000, the frequency of that haplotype will be: 2/2000 = 0.001. Reporting a Y haplotype frequency, without a confidence interval, is acceptable but only provides a factual statement regarding observations of a Y haplotype in the database. An upper confidence limit for the probability of the Y haplotype in the population should be calculated using the method described by Clopper and Pearson (1934). This uses the binomial distribution for the probabilities of counts, including zero or other small numbers that are found for Y haplotypes.


Databases

Forensic databases (without individual information, for frequency purposes): *
US Y-STR Database The United States of America (U.S.A. or USA), commonly known as the United States (U.S. or US) or America, is a country primarily located in North America. It consists of 50 states, a federal district, five major unincorporated territori ...
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*
Y Chromosome Haplotype Reference Database The Y Chromosome Haplotype Reference Database (YHRD) is an open-access, annotated collection of population samples typed for Y chromosomal sequence variants. Two important objectives are pursued: (1) the generation of reliable frequency estimates ...
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In
genetic genealogy Genetic genealogy is the use of genealogical DNA tests, i.e., DNA profiling and DNA testing, in combination with traditional genealogical methods, to infer genetic relationships between individuals. This application of genetics came to be used b ...
, Ysearch used to be the last sponsored database containing publicly submitted surnames and Y-STR
haplotypes A haplotype (haploid genotype) is a group of alleles in an organism that are inherited together from a single parent. Many organisms contain genetic material ( DNA) which is inherited from two parents. Normally these organisms have their DNA org ...
until its decommission on May 24, 2018, preceding by a day the implementation of the
General Data Protection Regulation The General Data Protection Regulation (GDPR) is a European Union regulation on data protection and privacy in the EU and the European Economic Area (EEA). The GDPR is an important component of EU privacy law and of human rights law, in partic ...
in the
European Union The European Union (EU) is a supranational political and economic union of member states that are located primarily in Europe. The union has a total area of and an estimated total population of about 447million. The EU has often been des ...
, following a prolonged period of lacking support from its creator,
Family Tree DNA FamilyTreeDNA is a division of Gene by Gene, a commercial genetic testing company based in Houston, Texas. FamilyTreeDNA offers analysis of autosomal DNA, YDNA, Y-DNA, and mitochondrial DNA to individuals for genealogical purpose. With a database ...
. The database was founded in 2003 and reached 219 thousand records (among which 152 thousand unique haplotypes) before its shutdown. Other similar databases had disappeared earlier.Ysearch
/ref> Haplogroup (Y-SNP) specific data:
Haplozone: The E-M35 Phylogeny Project (former E3b Project)


See also

*
List of Y-STR markers The following list of Y-STR markers are commonly used in forensic and genealogical DNA testing. DYS454 is the least diverse, and multi-copy marker DYS464 is the most diverse Y-STR marker. The location on the Y-chromosome of numbered Y-STR mark ...
*
Tandem repeat Tandem repeats occur in DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other. Several protein domains also form tandem repeats within their amino acid primary structure, such as armadil ...
*
Genealogical DNA test A genealogical DNA test is a DNA-based test used in genetic genealogy that looks at specific locations of a person's genome in order to find or verify ancestral genealogical relationships, or (with lower reliability) to estimate the ethnic mixt ...


References

{{Reflist


External links


Diagrams


National Institute of Standards and Technology (NIST)
— Y STR Positions along Y Chromosome


Fact sheets



— Summary List of Y Chromosome STR Loci and Available Fact Sheets

— STR Fact Sheets
dna.reinyday.com
— DYS464
Y-STR markers
— Details and statistics


Databases


yhrd.org
Y Chromosome Haplotype Reference Database The Y Chromosome Haplotype Reference Database (YHRD) is an open-access, annotated collection of population samples typed for Y chromosomal sequence variants. Two important objectives are pursued: (1) the generation of reliable frequency estimates ...

usystrdatabase.org
— U.S. Y-STR Database

— Applied Biosystems YFiler Database
ysearch.org
— Y-DNA database


Tutorials


Understanding Y-DNA Short Tandem Repeat (STR)Y-STR Marker TypesCalculation of Genetic Distance
Repetitive DNA sequences Genetic genealogy